
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   35 (   35),  selected   35 , name T0301TS464_3_1-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   35 , name T0301_D1.pdb
# PARAMETERS: T0301TS464_3_1-D1.T0301_D1.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       174 - 381         4.71    16.15
  LCS_AVERAGE:      5.54

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        60 - 64          1.71    25.64
  LONGEST_CONTINUOUS_SEGMENT:     5       178 - 182         1.36    30.75
  LONGEST_CONTINUOUS_SEGMENT:     5       181 - 380         1.94    15.97
  LONGEST_CONTINUOUS_SEGMENT:     5       384 - 388         1.59    28.06
  LONGEST_CONTINUOUS_SEGMENT:     5       386 - 390         1.93    19.97
  LCS_AVERAGE:      2.20

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       167 - 170         0.98    28.50
  LONGEST_CONTINUOUS_SEGMENT:     4       179 - 182         0.73    34.71
  LONGEST_CONTINUOUS_SEGMENT:     4       387 - 390         0.60    20.39
  LCS_AVERAGE:      1.67

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:  200
LCS_GDT     G      60     G      60      3    5   10     3    3    3    4    4    5    7    7    7    8   11   11   13   14   16   17   17   19   20   21 
LCS_GDT     M      61     M      61      3    5   10     3    3    3    4    4    5    7    7    7    9   11   12   13   14   16   17   17   19   20   21 
LCS_GDT     G      62     G      62      3    5   10     3    3    3    4    4    5    7    7    7    9   11   12   13   14   16   17   17   19   20   21 
LCS_GDT     G      63     G      63      3    5   10     1    3    3    4    4    5    7    7    7    8    8   12   12   14   16   17   17   19   20   21 
LCS_GDT     A      64     A      64      3    5   10     2    3    3    4    4    5    7    7    7    8    8    8    9   10   10   10   10   11   11   21 
LCS_GDT     G     166     G     166      3    3   11     3    3    3    4    5    6    7    8   10   10   11   12   16   17   18   19   22   23   23   24 
LCS_GDT     V     167     V     167      4    4   11     3    3    4    4    5    6    7    8   10   10   11   12   16   17   18   19   22   23   23   24 
LCS_GDT     T     168     T     168      4    4   11     3    3    4    4    4    4    7    8   10   10   11   12   16   17   18   19   22   23   23   24 
LCS_GDT     F     169     F     169      4    4   11     3    4    5    5    5    5    6    6    7   10   10   12   16   17   18   19   22   23   23   24 
LCS_GDT     P     170     P     170      4    4   11     0    4    5    5    5    5    6    8   10   10   11   12   16   17   18   19   22   23   23   24 
LCS_GDT     A     171     A     171      3    4   11     0    4    5    5    5    6    7    8   10   10   11   12   16   17   18   19   22   23   23   24 
LCS_GDT     A     172     A     172      3    4   11     0    3    3    4    4    5    6    7   10   10   11   12   16   17   17   19   22   23   23   24 
LCS_GDT     E     173     E     173      3    4   11     3    3    3    4    4    6    7    8   10   10   11   12   16   17   17   19   22   23   23   24 
LCS_GDT     I     174     I     174      3    3   13     3    3    3    4    5    5    6    8    8   10   11   12   16   17   18   19   22   23   23   24 
LCS_GDT     V     175     V     175      3    3   13     3    3    3    3    4    4    6    8    9   10   11   12   16   17   18   19   22   23   23   24 
LCS_GDT     L     176     L     176      3    3   13     3    3    3    3    3    4    7    8    8   10   11   12   16   17   18   19   22   23   23   24 
LCS_GDT     E     177     E     177      3    3   13     3    3    3    4    4    4    7    8    9   10   11   12   14   17   18   19   22   23   23   24 
LCS_GDT     F     178     F     178      3    5   13     3    3    4    5    5    5    7    8    9   10   10   11   13   16   18   19   22   23   23   24 
LCS_GDT     L     179     L     179      4    5   13     3    4    4    5    5    5    6    7    9   10   10   11   12   15   18   19   21   23   23   24 
LCS_GDT     D     180     D     180      4    5   13     3    4    4    5    5    5    6    6    6    8   10   11   12   12   14   15   18   20   23   24 
LCS_GDT     P     181     P     181      4    5   13     3    4    4    5    5    5    7    8    9   10   10   11   13   16   18   19   22   23   23   24 
LCS_GDT     S     182     S     182      4    5   13     2    4    4    5    5    5    7    8    9   10   10   11   13   16   18   19   22   23   23   24 
LCS_GDT     R     378     R     378      3    5   13     0    3    3    3    4    5    6    7    9   10   10   11   12   15   16   16   18   20   23   24 
LCS_GDT     S     379     S     379      3    5   13     0    3    3    3    4    5    6    7    9   10   10   11   12   15   18   19   22   23   23   24 
LCS_GDT     A     380     A     380      3    5   13     0    3    3    3    4    5    7    8    9   10   10   11   12   16   18   19   22   23   23   24 
LCS_GDT     R     381     R     381      3    3   13     1    3    3    3    3    4    7    8    8   10   11   12   16   17   18   19   22   23   23   24 
LCS_GDT     I     382     I     382      3    4    9     3    3    5    5    5    6    7    8   10   10   11   12   16   17   18   19   22   23   23   24 
LCS_GDT     L     383     L     383      3    4    9     3    3    4    4    5    5    6    8   10   10   11   12   16   17   17   19   22   23   23   24 
LCS_GDT     M     384     M     384      3    5    9     3    4    5    5    5    6    7    8   10   10   11   12   16   17   18   19   22   23   23   24 
LCS_GDT     E     385     E     385      3    5    9     0    3    4    4    5    6    6    7    8   10   11   12   16   17   17   19   22   23   23   24 
LCS_GDT     G     386     G     386      3    5    9     0    3    3    4    5    6    6    7    7    7   10   11   13   14   16   18   19   20   21   24 
LCS_GDT     W     387     W     387      4    5    9     3    4    4    4    5    6    6    7    7    7    7    9   10   11   12   14   14   16   19   21 
LCS_GDT     V     388     V     388      4    5    9     3    4    4    4    5    6    6    7    7    7    7    9   13   14   16   17   17   19   20   21 
LCS_GDT     R     389     R     389      4    5    9     3    4    4    4    5    6    6    7    7    7    7    9   13   14   15   17   17   18   19   21 
LCS_GDT     V     390     V     390      4    5    9     3    4    4    4    4    6    6    7    7    7    7    7    7   11   12   12   13   14   15   16 
LCS_AVERAGE  LCS_A:   3.14  (   1.67    2.20    5.54 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      3      4      5      5      5      6      7      8     10     10     11     12     16     17     18     19     22     23     23     24 
GDT PERCENT_CA   1.50   2.00   2.50   2.50   2.50   3.00   3.50   4.00   5.00   5.00   5.50   6.00   8.00   8.50   9.00   9.50  11.00  11.50  11.50  12.00
GDT RMS_LOCAL    0.02   0.60   1.04   1.04   1.04   2.07   2.39   2.68   3.14   3.14   3.42   3.89   5.04   5.21   5.97   6.12   6.49   6.65   6.65   6.86
GDT RMS_ALL_CA  30.48  20.39  11.79  11.79  11.79  16.72  16.55  17.03  17.18  17.18  17.43  15.89  13.78  13.29  12.45  12.47  12.13  12.19  12.19  12.27

#      Molecule1      Molecule2       DISTANCE
LGA    G      60      G      60         32.271
LGA    M      61      M      61         25.827
LGA    G      62      G      62         23.350
LGA    G      63      G      63         23.520
LGA    A      64      A      64         27.676
LGA    G     166      G     166          1.915
LGA    V     167      V     167          3.060
LGA    T     168      T     168          3.287
LGA    F     169      F     169          6.372
LGA    P     170      P     170          3.738
LGA    A     171      A     171          2.476
LGA    A     172      A     172          4.696
LGA    E     173      E     173          2.967
LGA    I     174      I     174          8.453
LGA    V     175      V     175         12.755
LGA    L     176      L     176         12.391
LGA    E     177      E     177         15.817
LGA    F     178      F     178         22.745
LGA    L     179      L     179         25.567
LGA    D     180      D     180         26.113
LGA    P     181      P     181         27.688
LGA    S     182      S     182         29.036
LGA    R     378      R     378         16.612
LGA    S     379      S     379         13.642
LGA    A     380      A     380         12.892
LGA    R     381      R     381          7.201
LGA    I     382      I     382          1.585
LGA    L     383      L     383          4.861
LGA    M     384      M     384          1.523
LGA    E     385      E     385          5.448
LGA    G     386      G     386          8.268
LGA    W     387      W     387         14.189
LGA    V     388      V     388         16.991
LGA    R     389      R     389         20.903
LGA    V     390      V     390         24.959

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   35  200    4.0      8    2.68     4.500     3.846     0.287

LGA_LOCAL      RMSD =  2.683  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 17.025  Number of atoms =   35 
Std_ALL_ATOMS  RMSD = 10.662  (standard rmsd on all 35 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.664583 * X  +   0.543215 * Y  +  -0.513076 * Z  +  88.818764
  Y_new =   0.680689 * X  +   0.156900 * Y  +  -0.715573 * Z  +  34.779160
  Z_new =  -0.308208 * X  +  -0.824803 * Y  +  -0.474033 * Z  +  52.378075 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.092422    1.049170  [ DEG:  -119.8870     60.1130 ]
  Theta =   0.313309    2.828283  [ DEG:    17.9513    162.0487 ]
  Phi   =   2.344223   -0.797370  [ DEG:   134.3141    -45.6859 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0301TS464_3_1-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_3_1-D1.T0301_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   35  200   4.0    8   2.68   3.846    10.66
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_3_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  GLY    60      66.351  12.656  17.330  1.00  0.00
ATOM      2  CA  MET    61      66.379  15.433  14.677  1.00  0.00
ATOM      3  CA  GLY    62      69.294  17.524  16.204  1.00  0.00
ATOM      4  CA  GLY    63      66.938  20.426  16.933  1.00  0.00
ATOM      5  CA  ALA    64      65.760  21.123  20.505  1.00  0.00
ATOM      6  CA  GLY   166      85.543  22.224  23.060  1.00  0.00
ATOM      7  CA  VAL   167      83.598  22.481  26.334  1.00  0.00
ATOM      8  CA  THR   168      80.866  24.648  24.810  1.00  0.00
ATOM      9  CA  PHE   169      80.365  21.982  22.163  1.00  0.00
ATOM     10  CA  PRO   170      80.186  19.245  24.801  1.00  0.00
ATOM     11  CA  ALA   171      77.374  21.508  26.048  1.00  0.00
ATOM     12  CA  ALA   172      75.212  21.043  22.906  1.00  0.00
ATOM     13  CA  GLU   173      75.866  17.300  23.093  1.00  0.00
ATOM     14  CA  ILE   174      74.540  17.077  26.655  1.00  0.00
ATOM     15  CA  VAL   175      71.520  19.258  25.874  1.00  0.00
ATOM     16  CA  LEU   176      70.705  17.466  22.582  1.00  0.00
ATOM     17  CA  GLU   177      71.022  14.045  24.273  1.00  0.00
ATOM     18  CA  PHE   178      68.520  14.985  26.995  1.00  0.00
ATOM     19  CA  LEU   179      65.898  17.091  25.290  1.00  0.00
ATOM     20  CA  ASP   180      65.867  15.957  21.691  1.00  0.00
ATOM     21  CA  PRO   181      63.166  13.333  22.032  1.00  0.00
ATOM     22  CA  SER   182      62.654  12.585  18.279  1.00  0.00
ATOM     64  CA  ARG   378      73.580  29.490  27.083  1.00  0.00
ATOM     65  CA  SER   379      69.908  28.805  26.337  1.00  0.00
ATOM     66  CA  ALA   380      69.699  32.256  24.761  1.00  0.00
ATOM     67  CA  ARG   381      72.609  31.728  22.375  1.00  0.00
ATOM     68  CA  ILE   382      71.439  28.318  21.200  1.00  0.00
ATOM     69  CA  LEU   383      67.991  29.810  20.779  1.00  0.00
ATOM     70  CA  MET   384      69.383  32.700  18.746  1.00  0.00
ATOM     71  CA  GLU   385      71.364  30.217  16.620  1.00  0.00
ATOM     72  CA  GLY   386      68.074  28.442  15.868  1.00  0.00
ATOM     73  CA  TRP   387      68.894  25.287  17.843  1.00  0.00
ATOM     74  CA  VAL   388      66.195  25.445  20.509  1.00  0.00
ATOM     75  CA  ARG   389      62.569  26.478  20.921  1.00  0.00
ATOM     76  CA  VAL   390      62.209  28.439  24.177  1.00  0.00
TER
END
